January 2018 - BBClist - maillist.psb.ugent.be

Early Bird deadline approaches for Applied Bioinformatics in Life Sciences (2nd), 8-9 March, Leuven
by Alexander Botzki 22 Jan '18

22 Jan '18

Dear colleague, The early bird registration for our VIB Applied Bioinformatics Conference is getting closer (25th of January)! More info: http://bit.ly/2hF3J59 #ABLS18 Hope to see many of you at the Irish College in Leuven! Best regards, Alexander Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be | @vibbioinfocore | https://corefacilities.vib.be

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Fwd: Postdoctoral position in Microbial Metagenomics and Bioinformatics
by Bas E. Dutilh 22 Jan '18

22 Jan '18

A metagenomics postdoc in Brazil, position open now: ---------- Forwarded message ---------- From: Pedro Meirelles <pedrommeirelles(a)gmail.com> Dear colleagues, We are looking for a highly motivated and talented postdoctoral researcher, specialized in metagenomics and sequence analysis. Candidates should have interest in working at the interface between bioinformatics, statistics, modeling and microbial ecology. In his/her role, he/she will lead the bioinformatics analysis working within an interdisciplinary and international team developing an exciting research project about the effects of Climate Changes on aquifers’ microbiomes. This project is funded by Serrapilheira Institute (https://serrapilheira.org) The project was designed to be done in four years. During the first year, we will analyze large publicly available metagenomic datasets. This year is crucial to have the other three years funded. If so, we will perform field and laboratory experiments, which will allow his/her computational results to be experimentally validated. I will be very grateful if you forward this email to your peers, Institutes/Departments and share our announcements in social media: https://www.facebook.com/meirelleslab https://twitter.com/MeirellesLab/status/953999031285506048 https://www.instagram.com/p/BeGDXPejDTO/ Applications deadline: February 20th For more information to apply please visit our website: http://meirelleslab.org/opportunities/postdoctoral-position-call/ [image: Imagem inline 1] Best wishes -- Pedro Milet Meirelles Associate Professor Institute of Biology Federal University of Bahia -- Dr. Bas E. Dutilh Metagenomics Group Theoretical Biology and Bioinformatics, Utrecht University Utrecht Bioinformatics Center +31 (0)30 253 4212 - http://tbb.bio.uu.nl/dutilh

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[ELIXIR-IIB] Software Carpentry Workshop - Milano (Italy), 22-23 Feb 2018 Inbox x
by Alexander Botzki 19 Jan '18

19 Jan '18

From: Elixir-ITA Training <elixir.ita.training(a)gmail.com> Subject: [Training-coordinators] REMINDER: [ELIXIR-IIB] Software Carpentry Workshop - Milano (Italy), 22-23 Feb 2018 COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. The University of Milano Bicocca (Italy) in collaboration with ELIXIR-IIB, is pleased to announce the upcoming Software Carpentry workshop. IMPORTANT DATES: Deadline for applications: 25 January 2018 Course date: 22-23 February 2018 FEE: 30€ A maximum of 30 candidates will be accepted in the course. Chosen participants will be notified by 27 January 2018; all information and payment details will be sent by email. VENUE: University of Milano-Bicocca (lab 716, floor 1, building U7, Via Bicocca degli Arcimboldi, 8 - 20126 Milano). COURSE DESCRIPTION: This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. In particular, in this workshop we will cover the Unix Shell, programming in Python and version control with Git. Full details at: https://elixir-iib-training.github.io/website/2018/02/22/SWC-Milano-Bicocca… Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training(a)gmail.com<mailto:elixir.ita.training@gmail.com>) and/or the local organiser Dr. Gianluca Della Vedova (gianluca(a)dellavedova.org<mailto:gianluca@dellavedova.org>). We apologise for cross-posting. Please, email us back with the word REMOVE as the subject line, if you don't want to receive messages from ELIXIR-IIB Training anymore. Kind regards, the Organisers. -- ELIXIR-IIB Training https://elixir-iib-training.github.io/website/ [Image removed by sender.]

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PostDoc in Computational Biology - Marseille, France
by Anaïs BAUDOT 15 Jan '18

15 Jan '18

Dear colleagues, We have an opening position for a postdoctoral fellow in the recently created network and systems biology group, in the Marseille Medical Genetics Unit. The project is dedicated to the study of neuroendocrine tumors thanks to interactome network and proteomics approaches. Please see attachement for more details, and feel free to forward this message to potential candidates. Best regards, Anaïs --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France anais.baudot(a)univ-amu.fr

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[Gtpb] ELB18F Entry Level Bioinformatics - course announcement
by GTPB Administration 10 Jan '18

10 Jan '18

ANNOUNCEMENT ELB18F Entry Level Bioinformatics (First course in 2018) our entry level course with a soft introduction to NGS data analysis with David P. Judge, Pedro L. Fernandes and Daniel Sobral The GTPB is proud to announce that the above referenced hands-on training course is open for applications Important dates IMPORTANT DATES for this Course Deadline for applications: February 8th 2018 Course dates: February 19th - February 23rd 2018 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. http://gtpb.igc.gulbenkian.pt/bicourses/2018/ELB18F Hoping that this course meets your interests, Pedro Fernandes -- Pedro L Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Last days to submit your abstract for Applied Bioinformatics in Life Sciences (2nd edition), 8-9 March, Leuven
by Lander Briels 08 Jan '18

08 Jan '18

8-9 March - Leuven - BE No Images? Click here<http://email.vibconferences.be/t/r-e-jrdryktt-l-f/> [http://i1.cmail19.com/ei/r/51/C55/137/031430/csfinal/Mailheaderwhiteletters…]<http://email.vibconferences.be/t/r-i-jrdryktt-l-r/> Abstract deadline 11 January Early Bird deadline 25 January Dear , First of all we wish you a happy and healthy new year! That all your goals may be achieved in 2018! With this email we want to remind you of the upcoming Abstract deadline of 11 January and would like to offer you the opportunity to take advantage of the Early Bird discount to register for the second edition of 'Applied Bioinformatics in Life Sciences'. The conference will take place on 8-9 March 2018, in Leuven, Belgium. [Rounded Rectangle: Register here] [Present your research at ABLS18]<http://email.vibconferences.be/t/r-i-jrdryktt-l-j/> Call for Abstracts - poster award Present your own research to more than 200 peers during one of our poster sessions. The deadline for the poster abstract submission is 11 January, 2018. The best abstracts will be selected for an oral presentation and the best poster will receive a poster prize! [Rounded Rectangle: Submit your abstract] [http://i3.cmail19.com/ei/r/51/C55/137/031430/csfinal/Speaker-hall1.jpg] Join 18 experts in the field The symposium will bring together some of the most highly regarded Academics in the world with novel technologies in several sessions, with topics focused on: · Medical Integrative Omics · Proteomics and Metabolomics · Structural Bioinformatics · Systems Biology The speakers covering these topics include: · Naama Barkai - Weizmann Institute of Science, IL · Stephan Beck - UCL, UK · Albert Heck - Utrecht University, NL · Ines Thiele - University of Luxembourg, LU · Janet Thornton - EMBL-EBI, UK · Michele Vendruscolo - University of Cambridge, UK · And many more...<http://email.vibconferences.be/t/r-i-jrdryktt-l-i/> [http://i4.cmail19.com/ei/r/51/C55/137/031430/csfinal/FacultyClub1.jpg] Meet your next collaborator You will also have ample opportunity to network during the catering moments and poster sessions. The conference dinner will take place in the 'The <http://email.vibconferences.be/t/r-i-jrdryktt-l-d/> F<http://email.vibconferences.be/t/r-i-jrdryktt-l-h/>aculty Club<http://email.vibconferences.be/t/r-i-jrdryktt-l-k/>' on 8 March. This is the ideal opportunity to network with our speakers and to meet your future collaborators. Not convinced yet? Please take a look at the pictures from the first edition<http://email.vibconferences.be/t/r-i-jrdryktt-l-b/>. We look forward to welcoming you in Leuven in 2018! With kind regards, Evy Vierstraete On behalf of the Organizing Committee: Alexander Botzki, VIB Bioinformatics Core Brigida Gallone, VIB-KU Leuven Center for Microbiology Diether Lambrechts, VIB-KU Leuven Center for Cancer Biology Joost Schymkowitz, VIB-KU Leuven Center for Brain & Disease Research Vanessa Vermeirssen, VIB-UGent Center for Plant Systems biology Paola Masuzzo, VIB-UGent Center for Medical Biotechnology Evy Vierstraete, VIB Science Events manager [Sponsors of GESB18]<http://email.vibconferences.be/t/r-i-jrdryktt-l-n/> [VIB Conference Series]<http://email.vibconferences.be/t/r-i-jrdryktt-l-x/> [Facebook]<http://email.vibconferences.be/t/r-i-jrdryktt-l-m/> [Twitter]<http://email.vibconferences.be/t/r-i-jrdryktt-l-c/> [LinkedIn]<http://email.vibconferences.be/t/r-i-jrdryktt-l-q/> [Website]<http://email.vibconferences.be/t/r-i-jrdryktt-l-a/> To stop receiveiving our invitations please click below. [http://i10.cmail19.com/static/eb/master/13-the-blueprint-3/images/tweet-ico…] Tweet <http://email.vibconferences.be/t/r-tw-jrdryktt-l-z/> [http://i1.cmail19.com/static/eb/master/13-the-blueprint-3/images/lishare-ic…] Share <http://email.vibconferences.be/t/r-li-jrdryktt-l-v/> Unsubscribe<http://email.vibconferences.be/t/r-u-jrdryktt-l-e/>

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bioinformatics postdoc in systems vaccinology
by Martijn.Huijnen＠radboudumc.nl 08 Jan '18

08 Jan '18

Dear all, The CMBI at the Radboud University is looking for a postdoc to do research into systems vaccinology of Bordetella pertussis (whooping cough, see attachment). Thank you for forwarding this vacancy to any potential candidates. Best regards, Martijn Huynen Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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One week left to apply: PhD position in bioinformatics for haplotype assembly - @DelftBL - @TUDelft
by Thomas Abeel - EWI 08 Jan '18

08 Jan '18

We have a Bioinformatics PhD position available at The Delft Bioinformatics Lab at TU Delft. Project: Your goal in this project is to create novel algorithms that resolve haplotypes in microbial genomes. Haplotypes refer to the sequence of all individual chromosome copies typically inherited together from a parent. This within-species genetic heterogeneity is one of the missing pieces in many microbial comparative genomics studies aiming to associate genotypes with phenotypes of interest. For many organisms, we poorly understand the contribution of the diversity within an individual, and one of the key reasons is that we don't have the computational tools to study this diversity. With the continued improvements in third generation sequencing technology, combined with the vast quantity of data being deposited publicly, this problem is ready for a solution. You will have three aims: • Implement reference-guided haplotyping from pangenome reference sequence graphs • Explore de novo haplotyping from 3rd generation sequencing data • Investigate copy-number detection at the gene and chromosome scale, and intra-chromosomal DNA variation. Candidate: The ideal candidate has an MSc degree in bioinformatics, computer science, or applied mathematics. Affinity with or experience in biology, genomics and/or sequence analysis are desirable. He/she must be able to work effectively in a multidisciplinary team. The candidate shares our view that communication skills are important, as is the ability to interact with peers, students, and technical staff. Programming and scripting experience is required. Experience in microbial genomics is an advantage. Apply before January 15, 2018 https://www.academictransfer.com/employer/TUD/vacancy/43973/lang/en/ kind regards, Thomas

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CFP META'18 @Marrakech
by El-ghazali Talbi 07 Jan '18

07 Jan '18

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. ********************************************************************** META'2018 International Conference on Metaheuristics and Nature Inspired Computing 27-31 Oct 2018 Marrakech, Morocco http://meta2018.sciencesconf.org/ ********************************************************************** META is one of the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, META’2018 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. All selected papers will be published in the conference proceedings. Following the tradition, selected long papers will be published in a postponed Springer book as in META'2014 and META'2016. At least, 2 special special issues in ISI and SCOPUS journals are also confirmed: - Special issue in "Optimization and learning" in Wiley Journal ITOR - International Journal on Operational Research (deadline for submission: 31 May 2018) - Special issue in "Metaheuristics for 4.0 industry" in Elsevier Journal Swarm-and-Evolutionary-Computation (deadline for submission: 31 May 2018) META'2018 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. META'2018 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. The scope of the META’2018 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm optimization, scatter search, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Parallel algorithms * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, cloud, bio-medical, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, … * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Hyper-heuristics, cross-domain metaheuristics * Software frameworks for metaheuristics and nature inspired computing Submission of papers: ____________________ - Submission of papers via the website S1) Short papers: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages. S2) Long papers: Original research contributions of a maximum of 10 pages. S3) Journal papers: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication. For this special case, the submission should have the same title that the accepted work, the abstract AND the complete reference of the work. - Proceedings of the conference will be provided. Selected papers of type S1 and S2 will be published in a Springer book and international journals (ISI journals). - Predefined styles are available on the website http://meta2018.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline 15th March 2018. contact meta2018(a)sciencesconf.org Important dates _______________ - Submission deadline: April 13, 2018 - Notification of acceptance: May 15, 2018

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Post doctoral position in Lund, machine learning in medicine
by Mauno Vihinen 04 Jan '18

04 Jan '18

We are seeking for compentent candidates to a position of post doctoral fellow at Lund University. The position is for two years with an immediate opening. Requirements and details are at available at https://lu.mynetworkglobal.com/en/what:job/jobID:181799/type:job/where:4/ap… Applications submitted only by the electronic system at university will be considered. This position is for a person to continue development of our highly accurate variation prediction methods including PON-P2, PON-MMR2, PON-mt-tRNA, PON-Sol and others. For further information, contact: -- Mauno Vihinen Professor of Medical Structural Biology Department of Experimental Medical Science Lund University BMC B13 SE-22184 Lund Sweden http://structure.bmc.lu.se tel +46 72 526 0022 ORCID iD 0000-0002-9614-7976

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